Web of Science: 75 cites, Scopus: 78 cites, Google Scholar: cites,
Exploring the gonad transcriptome of two extreme male pigs with RNA-seq
Esteve-Codina, Anna (Centre de Recerca en Agrigenòmica)
Kofler, Robert (Vetmeduni Vienna. Institut für Populationsgenetik (Viena, Àustria))
Palmieri, Nicola (Vetmeduni Vienna. Institut für Populationsgenetik (Viena, Àustria))
Bussotti, Giovanni (Universitat Pompeu Fabra)
Notredame, Cedric (Universitat Pompeu Fabra)
Perez-Enciso, Miguel (Centre de Recerca en Agrigenòmica)

Data: 2011
Resum: Background: Although RNA-seq greatly advances our understanding of complex transcriptome landscapes, such as those found in mammals, complete RNA-seq studies in livestock and in particular in the pig are still lacking. Here, we used high-throughput RNA sequencing to gain insight into the characterization of the poly-A RNA fraction expressed in pig male gonads. An expression analysis comparing different mapping approaches and detection of allele specific expression is also discussed in this study. Results: By sequencing testicle mRNA of two phenotypically extreme pigs, one Iberian and one Large White, we identified hundreds of unannotated protein-coding genes (PcGs) in intergenic regions, some of them presenting orthology with closely related species. Interestingly, we also detected 2047 putative long non-coding RNA (lncRNA), including 469 with human homologues. Two methods, DEGseq and Cufflinks, were used for analyzing expression. DEGseq identified 15% less expressed genes than Cufflinks, because DEGseq utilizes only unambiguously mapped reads. Moreover, a large fraction of the transcriptome is made up of transposable elements (14500 elements encountered), as has been reported in previous studies. Gene expression results between microarray and RNA-seq technologies were relatively well correlated (r = 0. 71 across individuals). Differentially expressed genes between Large White and Iberian showed a significant overrepresentation of gamete production and lipid metabolism gene ontology categories. Finally, allelic imbalance was detected in ~ 4% of heterozygous sites. Conclusions: RNA-seq is a powerful tool to gain insight into complex transcriptomes. In addition to uncovering many unnanotated genes, our study allowed us to determine that a considerable fraction is made up of long non-coding transcripts and transposable elements. Their biological roles remain to be determined in future studies. In terms of differences in expression between Large White and Iberian pigs, these were largest for genes involved in spermatogenesis and lipid metabolism, which is consistent with phenotypic extreme differences in prolificacy and fat deposition between these two breeds.
Ajuts: European Commission 222664
Ministerio de Ciencia e Innovación AGL2010-14822
Ministerio de Ciencia e Innovación PN2008-2011/BFU2008-00419
Ministerio de Ciencia e Innovación CSD2007-00036
Drets: Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original. Creative Commons
Llengua: Anglès
Document: Article ; Versió publicada
Publicat a: BMC genomics, Vol. 12, N. 552 (November 2011) , p. 1-14, ISSN 1471-2164

DOI: 10.1186/1471-2164-12-552
PMID: 22067327

14 p, 1.1 MB

Additional file 1
1 p, 41.1 KB

Additional file 4
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